True. But even in this case, the same code injection logic can apply (depending on where you make the changes). The IL itself can simply be seen as yet another platform.

A great example is Android - you can patch the .dex class files with Lucky Patcher (in cases where apktool smali changes cannot help you).

IL obfuscations may also be worked around by patching the IL code directly too, which depends on the use case again.

The gist always is - carve out a space for your own code. No matter the language, a computer program is a computer program.